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minor tweaks

This commit is contained in:
Heng Li 2017-06-06 15:31:21 -04:00
parent d816e48fce
commit a2958a4836
3 changed files with 7 additions and 7 deletions
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10
chain.c
View File

@ -19,7 +19,7 @@ static inline int ilog2_32(uint32_t v)
return (t = v>>8) ? 8 + LogTable256[t] : LogTable256[v];
}
int mm_chain_dp(int match_len, int max_dist, int bw, int max_skip, int min_sc, int n, mm128_t *a, uint64_t **_u, void *km)
int mm_chain_dp(int max_dist, int bw, int max_skip, int min_sc, int n, mm128_t *a, uint64_t **_u, void *km)
{
int32_t st = 0, i, j, k, *p, *f, *t, *v, n_u, n_v;
uint64_t *u;
@ -34,7 +34,7 @@ int mm_chain_dp(int match_len, int max_dist, int bw, int max_skip, int min_sc, i
// fill the score and backtrack arrays
for (i = 0; i < n; ++i) {
uint64_t ri = a[i].x;
int32_t qi = (int32_t)a[i].y;
int32_t qi = (int32_t)a[i].y, q_span = a[i].y>>32;
int32_t max_f = -INT32_MAX, max_j = -1, n_skip = 0;
while (st < i && ri - a[st].x > max_dist) ++st;
for (j = i - 1; j >= st; --j) {
@ -48,12 +48,12 @@ int mm_chain_dp(int match_len, int max_dist, int bw, int max_skip, int min_sc, i
}
dd = dr > dq? dr - dq : dq - dr;
if (dd > bw) continue;
sc = dq > match_len && dr > match_len? match_len : dq < dr? dq : dr;
sc = f[j] + sc - ilog2_32(dd);
sc = dq > q_span && dr > q_span? q_span : dq < dr? dq : dr;
sc = f[j] + sc - (dd? ilog2_32(dd) : 0);
if (sc > max_f) max_f = sc, max_j = j;
}
if (max_j >= 0) f[i] = max_f, p[i] = max_j;
else f[i] = match_len, p[i] = -1;
else f[i] = q_span, p[i] = -1;
}
// find the ending positions of chains

2
map.c
View File

@ -227,7 +227,7 @@ void mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b, uint3
kfree(b->km_fixed, m);
//for (i = 0; i < n_a; ++i) printf("%c\t%s\t%d\t%d\n", "+-"[a[i].x>>63], mi->seq[a[i].x<<1>>33].name, (uint32_t)a[i].x>>1, (uint32_t)a[i].y);
n_u = mm_chain_dp(mi->k, opt->max_gap, opt->bw, opt->max_skip, opt->min_score, n_a, a, &u, b->km_fixed);
n_u = mm_chain_dp(opt->max_gap, opt->bw, opt->max_skip, opt->min_score, n_a, a, &u, b->km_fixed);
printf("%s\t%d", qname, n_u);
for (i = j = 0; i < n_u; ++i) {
int n = (uint32_t)u[i];

2
mmpriv.h
View File

@ -14,7 +14,7 @@ void radix_sort_128x(mm128_t *beg, mm128_t *end);
void radix_sort_64(uint64_t *beg, uint64_t *end);
uint32_t ks_ksmall_uint32_t(size_t n, uint32_t arr[], size_t kk);
int mm_chain_dp(int match_len, int max_dist, int bw, int max_skip, int min_sc, int n, mm128_t *a, uint64_t **_u, void *km);
int mm_chain_dp(int max_dist, int bw, int max_skip, int min_sc, int n, mm128_t *a, uint64_t **_u, void *km);
#ifdef __cplusplus
}